As is known in the art, internal combustion engines with variable valve timing (VVT) are being introduced into the market place in an effort to improve fuel economy and emissions. As is also known in the art, engine controllers typically require an estimate of cylinder charge. Estimated cylinder charge is, however, significantly affected by valve timing. Furthermore, some such engines are equipped with cam profile switching (CPS), which depending on the various valve profiles, may also affect charge. The result is a significantly more complex charge estimation problem, as compared to conventional engine systems.